Merge pull request #26 from BMCV/develop

Update to v0.4.0

.devcontainer/devcontainer.json

@@ -3,7 +3,10 @@
 {
 	"name": "Python 3",
 	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
-	"image": "mcr.microsoft.com/devcontainers/python:0-3.8",
+	"image": "mcr.microsoft.com/devcontainers/python:0-3.11",
+	"containerEnv": {
+		"DOCKER_DEFAULT_PLATFORM": "linux/amd64"
+	},
 
 	// Features to add to the dev container. More info: https://containers.dev/features.
 	// "features": {},
@@ -12,13 +15,13 @@
 	// "forwardPorts": [],
 
 	// Use 'postCreateCommand' to run commands after the container is created.
-	"postCreateCommand": "pip3 install --user -r requirements.txt",
+	"postCreateCommand": "pip3 install -r requirements.txt",
 
 	// Configure tool-specific properties.
 	"customizations": {
 		"vscode": {
 			"settings": {
-				"python.analysis.extraPaths": ["/home/vscode/.local/lib/python3.8/site-packages"]
+				"python.analysis.extraPaths": ["/home/vscode/.local/lib/python3.11/site-packages"]
 			}
 		}
 	}

.flake8

@@ -0,0 +1,10 @@
+[flake8]
+
+max-line-length = 120
+
+extend-ignore = E221,E211,E222,E202,F541,E201,E203,E125,E272
+
+per-file-ignores =
+    superdsm/__init__.py:F401
+
+exclude = superdsm/_libs/**/*.py docs/source/conf.py

.github/workflows/linters.yml

@@ -0,0 +1,33 @@
+name: Linters
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches: ['*']
+
+jobs:
+
+  run_linters:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.11
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install flake8 isort
+
+    - name: Run linters
+      run: |
+        flake8 superdsm
+        flake8 tests
+        isort superdsm --check-only --diff
+        isort tests --check-only --diff

.github/workflows/regressiontests.yml

@@ -3,7 +3,7 @@ name: Regression tests
 on:
   workflow_dispatch:
   pull_request:
-    branches: ['develop']
+    branches: ['develop', 'master']
     paths:
       - .github/workflows/regressiontests.yml
       - superdsm/**
@@ -16,6 +16,7 @@ jobs:
 
   regression_tests:
     name: "Test: ${{ matrix.taskdir }}"
+    if: ${{ (github.event.action != 'synchronize' && github.event.action != 'opened') || github.event.pull_request.draft == false }}
     timeout-minutes: 1440
     runs-on: gpuagrohr-01
     container:
@@ -57,10 +58,10 @@ jobs:
 
       - name: Run SuperDSM
         run: |
-            python -m "superdsm.batch" examples --task-dir "${{ matrix.taskdir }}"
-            python -m "superdsm.batch" examples --task-dir "${{ matrix.taskdir }}" --run
+            python -m "superdsm" examples --task-dir "examples/${{ matrix.taskdir }}"
+            python -m "superdsm" examples --task-dir "examples/${{ matrix.taskdir }}" --run
         env:
-          SUPERDSM_INTERMEDIATE_OUTPUT: false
+          REPYPE_CLI_INTERMEDIATE: false
           SUPERDSM_NUM_CPUS: 20
 
       - name: Validate results

.github/workflows/testsuite.yml

@@ -3,14 +3,14 @@ name: Test suite
 on:
   workflow_dispatch:
   pull_request:
-    branches: ['develop']
+    branches: ['develop', 'master']
     paths:
-      - .github/workflows/testsuite.yml
-      - superdsm/**
-      - examples/**
-      - superdsm.yml
-      - tests/**
-      - requirements.txt
+      - '.github/workflows/testsuite.yml'
+      - 'superdsm/**'
+      - 'examples/**'
+      - 'superdsm.yml'
+      - 'tests/**'
+      - 'requirements.txt'
 
 jobs:
 
@@ -31,6 +31,9 @@ jobs:
       - name: Clear cache  # otherwise corrupted packages can be reported sometimes
         run: rm -rf /github/home/conda_pkgs_dir
 
+      - name: Install dependencies
+        run: apt-get update && apt-get install -y git
+
       - name: Setup Miniconda
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -41,5 +44,14 @@ jobs:
           activate-environment: superdsm
           environment-file: superdsm.yml
 
+      - name: Export the environment
+        run: 'conda env export | grep -v "^prefix: " > superdsm.yml'
+
+      - name: Save the environment as an artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: superdsm.yml
+          path: superdsm.yml
+
       - name: Run SuperDSM
         run: python -m "unittest"

.github/workflows/validate_pr.yml

@@ -31,7 +31,24 @@ jobs:
           apt-get update
           apt-get install -y ca-certificates
     
-      - uses: blend/[email protected]
+      - name: Wait for test suite
+        uses: blend/[email protected]
+        if: ${{ (github.event.action == 'synchronize' || github.event.action == 'opened') && github.event.pull_request.draft == true }}
+        with:
+          interval: 20s
+          timeout: 1440m
+          checks-yaml: |
+            - job: 'Test suite'
+              paths:
+                - .github/workflows/testsuite.yml
+                - superdsm/**
+                - examples/**
+                - superdsm.yml
+                - tests/**
+    
+      - name: Wait for test suite and regression tests
+        uses: blend/[email protected]
+        if: ${{ (github.event.action != 'synchronize' && github.event.action != 'opened') || github.event.pull_request.draft == false }}
         with:
           interval: 20s
           timeout: 1440m

.gitignore

@@ -2,6 +2,9 @@
 /build
 *.swp
 .DS_Store
+._.DS_Store
+/actual_csv
+/examples.regression
 /examples/**/*.csv
 /examples/**/*.gz
 /examples/**/.*.json
@@ -15,3 +18,5 @@
 /tests/data
 /tests/actual
 /tests/logs
+/.venv
+/docs/build

.isort.cfg

@@ -0,0 +1,11 @@
+[settings]
+
+multi_line_output = 3
+
+force_grid_wrap = 2
+
+include_trailing_comma = true
+
+skip_glob =
+    superdsm/_libs/**/*.py
+    docs/source/conf.py

.vscode/settings.json

@@ -0,0 +1,9 @@
+{
+    "[git-commit]": {
+        "editor.rulers": [50]
+    },
+
+    "[python]": {
+        "editor.rulers": [119]
+    }
+}

docs/source/conf.py

@@ -6,6 +6,11 @@
 copyright = '2017-2024 Leonid Kostrykin, Biomedical Computer Vision Group, Heidelberg University'
 author = 'Leonid Kostrykin'
 
+# -- Add directory which contains the project to sys.path
+import os, sys
+sys.path.insert(0, os.path.abspath('../..'))
+os.environ['PYTHONPATH'] = os.path.abspath('../..') + ':' + os.environ.get('PYTHONPATH', '')
+
 # -- General configuration
 
 extensions = [
@@ -14,12 +19,14 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.autosummary',
     'sphinx.ext.intersphinx',
+    'sphinx.ext.napoleon',
     'sphinx_autorun',
 ]
 
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3/', None),
     'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
+    'repype': ('https://repype.readthedocs.io/en/stable/', None),
 }
 intersphinx_disabled_domains = ['std']